Contacts of the strand formed by residues 88 - 93 (chain A) in PDB entry 2R2J
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MSE 88 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A PHE* 3.2 2.8 - - - -
85A ARG* 2.8 46.3 + - + +
86A ASN* 3.2 6.5 + - + +
87A GLY* 1.3 78.9 - - - +
89A MSE 1.3 73.9 + - - +
90A MSE 3.6 4.0 + - - +
151A ARG* 4.7 10.8 - - - +
155A ILE* 3.5 22.2 - - + -
201A PHE* 3.5 39.5 - - + -
205A TYR* 6.1 2.7 - - - -
380A SIN 4.9 10.3 - - - +
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Residues in contact with MSE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ARG 5.8 0.2 - - - +
73A TYR* 3.6 34.8 - - + +
74A ARG* 2.6 39.9 - - - +
82A LYS* 3.4 40.6 - - + +
83A LEU 3.6 4.0 - - - +
84A PHE* 3.5 28.9 - - + -
87A GLY 3.9 0.4 + - - -
88A MSE 1.3 79.5 - - - +
90A MSE 1.3 76.4 + - - +
91A LYS* 3.6 3.0 + - - +
380A SIN 3.6 12.1 - - - +
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Residues in contact with MSE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LYS* 4.1 10.2 + - - +
83A LEU* 2.7 46.1 + - + +
84A PHE 4.5 0.2 - - - +
85A ARG* 3.5 33.4 - - + +
88A MSE 4.5 4.9 - - - +
89A MSE 1.3 88.7 - - - +
91A LYS* 1.3 63.4 + - - +
92A ARG 3.2 15.1 + - - +
110A GLN* 5.3 2.7 - - - +
154A ASN 4.0 2.2 - - - +
155A ILE* 3.4 50.9 - - + +
157A HIS* 6.1 0.2 - - + -
380A SIN 3.5 25.4 - - - +
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ARG* 6.0 1.1 - - - +
82A LYS* 4.6 5.6 + - - +
89A MSE 3.6 4.7 + - - -
90A MSE 1.3 71.8 - - - +
92A ARG* 1.3 62.5 + - + +
93A GLU* 3.8 5.5 + - - +
209A GLN* 4.6 15.4 - - - +
213A VAL* 5.5 6.3 - - - +
217A ARG* 4.6 9.3 - - - +
226A GLU* 3.2 17.7 - - - +
230A GLU* 4.2 25.1 + - + -
379A FMT 5.4 5.2 + - - -
380A SIN 3.1 45.8 + - + +
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Residues in contact with ARG 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LYS* 5.6 0.2 - - - -
83A LEU* 4.6 7.3 + - - +
90A MSE 3.7 17.8 - - - +
91A LYS* 1.3 81.3 - - + +
93A GLU* 1.3 67.1 + - - +
106A TYR* 4.6 7.1 + - - +
155A ILE 5.3 3.0 + - - -
158A ASP* 4.1 23.9 + - - +
159A ASP* 2.8 42.8 + - - -
222A GLU* 5.9 0.4 + - - -
223A ASN* 5.1 12.7 - - - +
226A GLU* 3.2 22.4 - - + +
380A SIN 3.1 29.0 + - - +
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ARG 5.4 2.1 - - - +
76A SER* 5.4 1.7 + - - -
77A LYS* 2.8 27.5 + - - -
80A THR* 3.5 21.0 - - - +
81A LEU 3.6 13.2 + - - +
82A LYS* 3.0 36.7 + - + +
83A LEU 5.5 0.2 - - - +
91A LYS 4.4 2.5 - - - +
92A ARG* 1.3 81.9 - - - +
94A TYR* 1.3 63.6 + - - +
95A ARG* 3.1 35.9 + - + +
106A TYR* 4.3 5.3 + - - -
226A GLU* 2.6 18.9 + - - +
229A GLU* 4.5 2.1 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il